I started having an intermittent problem this summer with my 2006 MCS conv. I hear it mainly when the car is idling. I can make it disappear by depressing the clutch pedal and letting it out slowly. At first i thought the throwout bearing was to blame, but then I found this youtube video (that's exactly the same noise my car is making) https://www.youtube.com/watch?v=JNXA-d5fovk. Some of the comments seem to suggest it's the dual mass flywheel.
Clutch doesn't seem to slip. I get the occasional chewbacca growl from the flywheel, and an annoying squeek when pressing the clutch pedal that I can't seem to get rid of with any type of lub.

 

I have a solid flywheel setup using the Valeo solid flywheel conversion kit and get a similar noise at idle.

I think I've read elsewhere that many folks consider it a normal sound for the transmission and it's just the gears or syncros lightly vibrating/chattering. The reason it goes away when you depress the clutch pedal is the internals of the transmission stop spinning. Unless you start getting other symptoms of something wrong, I'd say everything is probably okay.

 

From my understanding it's normal! I had a 2009 SRT-4 Caliber before the R53 and it had the dual mass flywheel and done the exact same thing. So I have learned to live with it.

 

I'm in a similar situation as you. Experienced the same symptoms you describe with 139k miles on the original clutch/flywheel. Now @144k miles, the clutch is beginning to slip a little, shifting gears are not as smooth at times, all on top of the rattling sound at idle. Pedal pressure isn't much different compared to before and brake fluid isn't leaking from the master or slave cylinders. The pedal squeak I silenced by spraying penetrating lube at the point where the pedal swings under the dash and rubbed sil-glyde where the master cylinder ball pushes against.

I've ordered a clutch kit, guide, and slave at this point. The cause of the sound is within the transmission and I'm not sure there's anything that can supress it from the outside. From others experiences, the flywheel or throwout bearing caused the problem. Either way, the transmission needs to get pulled.